Quality Filters
The Quality Filters allow one to filter variants by variant quality metrics. The filter can operate in a Simple or Advanced mode.
Modes
Simple
Select a minimum degree of sequencing Quality (Low, Moderate, High).
Advanced
For SNVs and Indels:
Select a minimum degree of sequencing Quality (Low, Moderate, High),
Define minimum Mapping Quality (0-60 - value can be exceeded using the text box),
Specify minimum Depth (0-500 - value can be exceeded using the text box),
Set minimum number of alternate reads in Alternate Read (0-500 - value can be exceeded using the text box). Note: available for cases run with pipeline version 5.26+.
Set limits on Allele bias (0-100). Note: when applied to mtDNA variants, the Allele bias filter operates on heteroplasmy levels.
For CNVs:
Set limits on CNV Length (50bp, 1kb, 10kb, 100kb, 1Mb, 100Mb, Max CNV length),
Set minimum CNV Bin Count (1, 5, 10, 25, 50, 100, 500).
Default values
When Filters are Reset to Default, The Quality Filters are set to:
Quality: Moderate and High,
Mapping Quality ≥45,
Depth ≥ 10,
Alternate Read - no filtering,
Allele bias - no filtering,
CNV Length - no filtering,
CNV Bin Count - no filtering.
As of version 2.26:
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